BioC experimental data: CHECK report for encoDnaseI on perceval

Package: encoDnaseI

Version: 0.1.18

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch encoDnaseI_0.1.18.tar.gz

StartedAt: 2014-04-04 10:35:33 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 10:57:47 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 1334.0 seconds

RetCode: 0

Status:  OK

CheckDir: encoDnaseI.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/encoDnaseI.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘encoDnaseI/DESCRIPTION’ ... OK
* this is package ‘encoDnaseI’ version ‘0.1.18’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘encoDnaseI’ can be installed ... [44s/46s] OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘GGBase’ ‘GGtools’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
makeHg18track: warning in matrix(dataVals, nc = 1): partial argument
  match of 'nc' to 'ncol'
WRC: warning in matrix(ans, nr = 2): partial argument match of 'nr' to
  'nrow'
[,hg18track-ANY-ANY-ANY: warning in matrix(dataVals(x)[kpinds], nc =
  1): partial argument match of 'nc' to 'ncol'
ALICOR: no visible binding for global variable ‘rawCD4’
WRC: no visible binding for global variable ‘d19’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Error in .requirePackage(package) : 
    unable to find required package 'snpMatrix'
  Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [30s/30s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
hg18track-class 5.546  0.113   5.795
encoDnaseI      4.909  0.116   5.026
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘SNPlocs.Hsapiens.dbSNP.20090506’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/encoDnaseI.Rcheck/00check.log’
for details.

* installing *source* package ‘encoDnaseI’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (encoDnaseI)

name	user	system	elapsed
encoDnaseI	4.909	0.116	5.026
hg18track-class	5.546	0.113	5.795
juxtaPlot	0.582	0.016	0.599